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A simple CLI toolbox to use the European Nucleotide Archive (ENA)

Project description Documentation Status

ena-utils is a small python package that provides a CLI to submit nucleotides sequences to the European Nucleotide Archive (ENA).

The goals of this package are:

  1. To facilitate the submission of large numbers of objects

  2. To ease the exploitation of the ENA metadata schema to its full potential (see the Future developments section below)

This is an early development version that provides only minimal features.

Supported submission types

  • Non-multiplexed paired-end sequencing reads


  • File upload

  • Study registration

  • Experiment registration

  • Run registration

  • Sample registration


  • Python3

  • Webin account


The latest release is available on PyPI and can be installed using pip:

$ pip install ena-utils

Isolated environments using pipx

Install and execute ena-utils in an isolated environment using pipx.

Install pipx and make sure that the $PATH is correctly configured.

$ python3 -m pip install --user pipx
$ pipx ensurepath

Once pipx is installed use following command to install ena-utils.

$ pipx install ena-utils
$ which ena-utils


The latest documentation is available at

Future developments

  • Auto-generation of the CLI and objects lists templates from the ENA schema XSD files.

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